Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 307 records · Page 17Linked to original sources

bioRxiv2025

Human-specific tandem repeat in CACNA1C modulates responses to neuronal stimulation

The recent development of long-read sequencing has made it possible to catalog variable number tandem repeats (VNTRs) in the human genome. However, little is known about their functional consequences. Here, we characterized the effect of TRACT, a VNTR that is unique to humans and that has sequence variants linked to risk for bipolar disorder and schizophrenia. By adding or removing this VNTR in both mouse models and human neural organoids, we find that TRACT, which is intronic to the L-type voltage-gated calcium channel gene CACNA1C, increases intracellular calcium after neuronal stimulation and leads to widespread changes in activity-dependent transcription programs in neurons. TRACT-dependent changes are enriched for genes associated with synapse formation and plasticity, and partially recapitulate evolutionary changes in activity-dependent transcription between species. These findings demonstrate that a single, human-specific, non-coding element can strongly affect the neuronal response to stimulation, and motivate the study of VNTRs as a genetic source of phenotypic variation in both evolution and disease.

genetics↗

bioRxiv2025

ATF4 alleviates doxorubicin-induced cardiomyopathy through H2S-mediated antioxidation

BackgroundDoxorubicin (DOX) remains a cornerstone in the treatment of various cancers. However, its clinical utilization is significantly hampered by dose-dependent cardiotoxicity. The generation of reactive oxygen species (ROS) constitutes the central component of the pathogenesis of DOX-induced cardiotoxicity. Activating transcription factor 4 (ATF4) has been demonstrated to exert a cardioprotective effect and augment cardiac antioxidative capacity in settings of heart failure. However, the role of ATF4 in DOX-induced cardiomyopathy (DIC) remains unknown. MethodsTo explore the role of ATF4 in DOX-induced cardiomyopathy, cardiac-specific ATF4 conditional heterozygous mice and AAV9 mediated ATF4 overexpression mouse models were utilized. Cardiac function was assessed by echocardiography. The upstream regulator and downstream mediator of ATF4 were evaluated using RNA-seq analysis and further verified using ChIP assay and luciferase reporter assay. ResultsWe found a substantial decrease in ATF4 expression levels in the heart of DIC mice. ATF4+/- mice exhibited a higher degree of susceptibility to DOX-induced cardiotoxicity in comparison with ATF4flox/flox mice, as evidenced by the manifestation of more severe cardiac dysfunction and a significantly earlier mortality rate. In contrast, cardiacc-specific overexpression ATF4 by AAV9 confers robust cardioprotection against DOX-induced cardiomyopathy. Mechanistically, we identified the upstream regulator of ATF4 as KLF16, which was significantly suppressed during DOX treatment. Further, the decrease of ATF4 led to a reduction in cystathionine {gamma}-lyase (CSE) transcription and hydrogen sulfide (H2S) production in the context of DOX-induced cardiotoxicity. ChIP and luciferase reporter assays revealed that ATF4 functioned as the transcription factor of the CSE gene, which is a key enzyme in the synthesis of H2S to counteract oxidative stress. Consistently, ROS scavengers or H2S donors was shown to mitigate the consequences of ATF4 deficiency. In contrast, the ectopic expression of ATF4 mitigated oxidative stress and apoptosis in DOX-induced cardiotoxicity, both in vivo and in vitro. ConclusionsOur study revealed a novel function of ATF4 in counteracting oxidative stress in DOX cardiotoxicity by promoting the transcription of CSE. ATF4 may represent a promising therapeutic target for the treatment of DOX-induced cardiomyopathy.

pathology↗

bioRxiv2025

Chondrolectin regulates the sublaminar localization and regenerative function of muscle satellite cells in mice

Skeletal muscle satellite cells (SCs) reside between the myofiber sarcolemma and basal lamina, where extracellular matrix (ECM) interactions are essential for their maintenance and regenerative function. Here, we identify chondrolectin (CHODL), a type I transmembrane protein with a C-type lectin domain, as a critical regulator of SC biology. Single-cell RNA-seq analysis reveals that Chodl is highly enriched in quiescent SCs but downregulated in proliferating myoblasts. Using conditional knockout models, we show that deletion of Chodl in embryonic myoblasts (ChodlMKO) or adult SCs (ChodlPKO) does not affect muscle development but markedly impairs regeneration in both young and aged mice. Chodl-deficient SCs exhibit reduced self-renewal, diminish proliferation, and impair differentiation, leading to defective myofiber repair. In silico network perturbation further predicts disruption of ECM-ligand interactions and Notch signaling, consistent with our observation that a significant fraction of SCs in ChodlPKOmice localize outside the basal lamina and undergo precocious activation. Together, these findings establish CHODL as a key determinant of SC niche localization and regenerative function, uncovering a previously unrecognized mechanism linking ECM interactions to muscle stem cell maintenance and repair.

developmental biology↗

bioRxiv2025

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data

Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) profiles chromatin accessibility at cellular resolution, making it possible to reveal epigenomic landscapes that govern gene regulation in a variety of cells. Nevertheless, heterogeneous feature spaces and complex processing pipelines have impeded the construction of an ensemble resource capable of supporting diverse downstream analytical scenarios. To address this gap, we present Human-scATAC-Corpus (https://health.tsinghua.edu.cn/human-scatac-corpus/), a comprehensive database of human scATAC-seq comprising 5,407,621 cells from 35 datasets across 37 tissues or cell lines. To support complementary use cases, each dataset is distributed in three aligned formats: cell-by-candidate cis-regulatory element matrices for cross-dataset integration, raw fragment files for flexible processing, and cell-by-peak matrices for within-dataset analyses. This resource spans diverse biological contexts and includes rich metadata, enabling method benchmarking and development, as well as pretraining of foundation models. The website offers searchable browsing, detailed dataset pages, on-demand downloads, and tutorials. EpiAgent, a foundation model pretrained on Human-scATAC-Corpus, is further integrated to provide online analyses, including reference mapping, embedding extraction, and cell type annotation. Human-scATAC-Corpus establishes a unified and scalable substrate for single-cell epigenomics and is intended to accelerate discovery while standardizing evaluation across tasks. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/674505v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@e2c4c3org.highwire.dtl.DTLVardef@1e3eaf8org.highwire.dtl.DTLVardef@5768c1org.highwire.dtl.DTLVardef@9e96ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Protective immunity against malaria by a nanoparticle CIS43-based junctional vaccine alone or in combination with R21

Repetitive display of the major repeats of the Plasmodium falciparum circumsporozoite protein (PfCSP) is the basis for two WHO-recommended vaccines: RTS,S/AS01 and R21/Matrix-M. Recently, however, the CIS43 monoclonal antibody that preferentially targets the junctional region of PfCSP has been shown to be highly protective in humans, highlighting its junctional epitope as a key vaccine target. Here, we develop a vaccine based on the tandem repeats of the junctional epitope displayed on a self-assembling nanoparticle, and compare this CIS43-based junctional vaccine alone or in combination with the benchmark R21 vaccine, using both B cell analysis and monoclonal antibody isolation to define targeting of the immune response. Comparable reduction in liver burden was observed following vaccination with junctional and R21 vaccines at a dose of 1 g. At a dose of 0.25 g, a modest reduction of malaria-liver burden with the junctional vaccine was observed compared to R21. Further, combining junctional and R21 vaccines induced modestly enhanced protection compared to either vaccine alone. While the R21 vaccine elicited antibodies primarily against the major repeats, the junctional vaccine elicited antibodies against both junctional and major repeat regions. In vivo-B cell analysis and isolation of monoclonal antibodies confirmed differences in vaccine-induced antibody specificities. Altogether, these data suggest the nanoparticle-formatted tandem-repeated CIS43-junctional vaccine to be a promising approach to broaden immunity against malaria, either as a standalone intervention or in combination with R21. HIGHLIGHTSO_LIDeveloped a self-assembling nanoparticle-displayed junctional vaccine of PfCSP based on tandem repeats of the epitope preferentially targeted by the highly protective CIS43 antibody C_LIO_LIThe CIS43-based junctional vaccine at low doses significantly reduced liver burden following malaria challenge in mice C_LIO_LIFollowing either low or high doses of the junctional vaccine in naive mice, adoptively transferred B cells expressing the CIS43 inferred germline sequence yielded a high frequency of germinal center and ASC responses C_LIO_LIThe CIS43-based junctional vaccine elicits antibodies against junctional and major repeat regions whereas the R21 vaccine elicits responses primarily against the major repeat region C_LIO_LIAt low dose, the CIS43-based junctional vaccine given together with the R21 vaccine showed modestly improved control of liver burden compared to either vaccine alone C_LI

immunology↗

bioRxiv2025

Interferon gamma signaling drives cardiac metabolic rewiring

BackgroundIFN-gamma (IFN-{gamma}) signaling influences myocardial inflammation and fibrosis across a wide range of conditions, including ischemic and non-ischemic heart failure (HF). However, the direct effects of IFN-{gamma} on cardiomyocytes remain poorly understood. Here, we developed a novel in vivo model to investigate how IFN-{gamma} impacts myocardial metabolism and function. MethodsMale C57BL/6J mice were injected intravenously with hepatotropic adeno-associated virus (AAV2/8) carrying Ifng and nLuc reporter under the albumin promoter (AAV- Ifng) or empty vector control virus (AAV-ctrl). Cardiac alterations were monitored on day 28 through flow cytometry, bulk RNA sequencing, targeted metabolomics, isolated mitochondrial activity, echocardiography, and in vivo imaging using [18F]fluordeoxyglucose ([18F]FDG) and [18F]fluoro-6-thia-heptadecanoic acid. Additionally, mice lacking IFN-{gamma} receptor expression in cardiomyocytes (Myh6Cre Ifngr1fl/fl) were used to further dissect the cell-intrinsic roles of IFN-{gamma} signaling in cardiomyocyte metabolic reprograming. ResultsAfter confirming liver-specific viral transfection and elevated serum IFN-{gamma} production at physiological levels, we observed cardiac metabolic adaptation and rewiring in animals treated with AAV-Ifng compared to control animals. Myocardial bulk RNA sequencing and gene set enrichment analysis identified an IFN-{gamma} response signature accompanied by marked down-regulations of oxidative phosphorylation and fatty acid oxidation pathways. Functional assessment of isolated cardiac mitochondria showed decreased oxygen consumption, and targeted metabolomics confirmed metabolic shifts toward glycolysis in mice overexpressing IFN-{gamma}. In vivo imaging confirmed increased cardiac glucose uptake following AAV-Ifng treatment. Notably, these metabolic alterations were abrogated in mice with cardiomyocyte-specific deletion of IFN-{gamma} receptors (IFNGR). ConclusionsSystemic IFN-{gamma} induces pronounced metabolic reprogramming in the heart, characterized by increased glucose uptake and reduced oxidative phosphorylation, via direct signaling through cardiomyocyte IFNGR. These alterations mirror those observed in aging and some forms of HF, thereby highlighting that, beyond classical inflammation, this cytokine regulates cardiac metabolism. Novelty and significanceO_ST_ABSWhat is known?C_ST_ABSO_LIImmunological mechanisms can impact myocardial disease progression through complex context-dependent mechanisms. C_LIO_LIIFN-{gamma}, a cytokine primarily secreted by natural killer and T cells, promotes myocardial inflammation and fibrosis in the context of autoimmune myocarditis, pressure-overload-induced heart failure, and Chagas cardiomyopathy. C_LIO_LICytokines exert pleiotropic effects and can influence inflammatory responses through mechanisms involving control of energy metabolism. C_LI What new information does this article contribute?O_LIA novel adeno-associated virus model of systemic IFN-{gamma} elevation allows assessment of cardio-immune-metabolic crosstalk without confounding factors. C_LIO_LIIFN-{gamma} drives cardiac metabolic reprogramming in inflammatory contexts, characterized by enhanced glucose uptake and glycolysis with mitochondrial dysfunction, ultimately altering cardiac metabolic fluxes and function. C_LIO_LIThe IFN-{gamma}-induced cardiac metabolic reprogramming is, at least in part, mediated through direct signaling via receptors on cardiomyocytes. C_LI

immunology↗

bioRxiv2025

Identification of stripe rust adult plant resistance genes in the hard winter wheat cultivar Bakers Ann

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most destructive wheat diseases. Identifying resistance genes is crucial for the development of resistant cultivars. "Bakers Ann", a hard winter wheat cultivar developed by Oklahoma State University, has shown durable adult plant resistance to stripe rust. To dissect the genetic basis underlying stripe rust resistance in Bakers Ann, 125 doubled haploid lines, derived from the cross OK12D22004-016 x Bakers Ann, were evaluated at the adult plant stage in the greenhouse and in field environments in Oklahoma, Kansas, and Washington. This population was genotyped using genotyping-by-sequencing, which produced 7,268 single-nucleotide polymorphisms for genetic mapping. Quantitative trait loci (QTL) analysis identified six loci, four from Bakers Ann on chromosomes 2DL, 4BS, 4BL, and 7BL, and two from OK12D22004-016 on chromosomes 2AS and 2AL. Although OK12D22004-016 is susceptible in the US Great Plains, it was found to carry QYr.osu-2AS, which was linked to Yr17 on the 2NvS translocation and explained up to 30% of the phenotypic variation, but was effective in a single location in Washington. Two major QTL were identified in Bakers Ann, QYr.osu-2DL on chromosome 2DL that explained up to 57% of the phenotypic variation and mapped close to Yr54, and QYr.osu-4BL on chromosome 4BL that explained up to 15% of the phenotypic variation and mapped close to Yr62. Resistance in Bakers Ann resulted from additive effects of the four QTL. Two kompetitive allele-specific PCR markers were developed for QYr.osu-2DL to facilitate marker-assisted selection for stripe rust resistance.

genetics↗

bioRxiv2025

Multiscale modeling of cell-substrate adhesion dynamics: effects of integrin activation, clustering and internalization

Cell adhesion is a fundamental biological process that governs cell proliferation, differentiation, migration, and tissue development. Cells adhere to the extracellular matrix through specialized transmembrane proteins, whose structures and functions are well studied. However, how mechanical, chemical, and biological factors interact to regulate these proteins and hence to shape cross-scale adhesion dynamics from molecular clustering to cellular migration remains unclear. Here, we propose a multiscale mechano-biochemical coupling framework to investigate the dynamics of cell-substrate adhesions, incorporating comprehensive molecular steps in the integrin life cycle, including activation, clustering, signal transduction and internalization. Our model elucidates the roles of caveolin transport and actin flow in modulating integrin dynamics and FA morphology. We identify the antagonistic interplay between integrin internalization and clustering that governs cross-scale adhesion dynamics. Furthermore, our model quantitatively demonstrates how the substrate stiffness regulates the integrin clustering size and internalization rate. These findings provide mechanistic insights into the regulation of cell migration, particularly the transition between durotaxis and negative durotaxis, driven by intracellular and extracellular microenvironmental factors. Our model offers an effective framework for understanding the cross-scale regulation process of cell adhesion involved in physiological and pathological activities, such as stem cell differentiation and cancer metastasis.

biophysics↗

bioRxiv2025

A comprehensive RNA virome from molluscan transcriptomes reveals extensive diversity and modular genome evolution

Mollusca is the second-largest animal phylum and an important marine food resource for humans. While DNA viruses that threaten molluscan aquaculture have received much attention, molluscan RNA viromes remain poorly explored. Here, based on 223 molluscan metatranscriptomes covering eight animal classes, we identified 80 species-level RNA viruses spanning three viral phyla and nine viral families. Phylogenetic result combined structural modeling found a major increase in the number of Pisuviricota-related lineages. Extensive modular evolution in viral genomes was observed including gene rearrangements and co-evolution of capsid and RdRP genes. Host prediction linked 78% of the RNA viruses to a diverse range of eukaryotes, including vertebrates, invertebrates, and algae. These findings expand the known diversity of RNA viruses in molluscs and shed light on their phylogenetic relationships, highlighting molluscs as valuable models for RNA virus evolution. Graphical abstractRNA virus diversity within 223 molluscan transcriptome samples were analyzed based on RdRP identification. Viruses belonging to the phylum Pisoviricota were the most abundant; co-evolution between RdRP and capsid proteins of molluscan Picornavirales was revealed, and a complex virus-host interaction network was constructed. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/673676v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1ce8fc0org.highwire.dtl.DTLVardef@3f9068org.highwire.dtl.DTLVardef@121cc2forg.highwire.dtl.DTLVardef@1e431a0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIComprehensive metatranscriptomic analysis found extensive RNA viral diversity in molluscs. C_LIO_LIPisuviricota dominate the molluscan RNA virome, substantially broadening known viral lineages. C_LIO_LIModular genome evolution involving gene rearrangements and conserved structural features characterize molluscan RNA viruses. C_LIO_LIMolluscs potentially serve as major ecological reservoirs for diverse RNA viruses infecting various eukaryotic hosts. C_LI

bioinformatics↗

bioRxiv2025

Combining Selenocystine Based Fluorescence Assay with Structural Prediction for Enhanced Detection and Analysis of Cystine Stone Pathology

BackgroundCystine stones, a rare but recurrent type of kidney stones, primarily result from cystinuria, an inherited disorder caused by mutations in the genes SLC3A1 and SLC7A9, which encode renal cystine transporters. These mutations impair cystine reabsorption, resulting in elevated urinary cystine concentrations and stone formation. Current diagnostic methods are limited, particularly for detecting molecular-level dysfunctions. We aimed to develop a nonradioactive method for functional assessment of cystine transporters and mutation-specific pathologies. MethodsWe designed an innovative diagnostic approach combining a selenocystine-based fluorescence assay with structural predictions using AlphaFold to rapidly and accurately assess cystine transporter function and the molecular impacts of genetic mutations. ResultsOur assay demonstrated comparable transport efficiencies of cystine and selenocystine by the SLC3A1/SLC7A9 complex, and effectively differentiated mild, moderate, and severe functional impairments associated with known clinical mutations, including A354T and P482L. Structural modeling further provided mechanistic insights into mutation-induced dysfunctions. ConclusionThis integrated approach--combining a sensitive selenocystine fluorescence assay with AI-powered structural analysis--enables rapid, precise diagnosis of cystinuria variants and delivers mechanistic insights for personalized therapeutic strategies.

genetics↗

bioRxiv2025

Breaking Free from the Acquisition Dogma for Volume Electron Microscopy

Volume electron microscopy (VEM) enables nanometer-resolution three-dimensional (3D) visualization of biological specimens via serial sectioning and imaging. Owing to precautions against additional challenges in downstream analysis, VEM datasets are often acquired unnecessarily at slow speeds and high resolutions, thereby limiting achievable imaging throughput. By systematically searching for optimal VEM acquisition conditions, we find that sufficient spatial resolution effectively counteracts high image noise in preserving 3D structural information. To further verify that denoising is more effective in restoring volumetric datasets than axial interpolation, machine learning-based methods, including a newly developed 3D context-based denoising model, were compared through various tasks on VEM datasets acquired simultaneously. Our volumetric approach not only outperforms other baseline methods in faithful feature recovery but also facilitates robust serial block-face cutting down to 20 nm by allowing fast imaging. This work provides both an optimized acquisition strategy and volumetric denoising methods as actionable guidelines for maximizing VEM throughput.

bioinformatics↗

bioRxiv2025

Loss of the Y chromosome drives cancer metabolic reprogramming

Metabolic reprogramming promotes cancer aggressiveness and an immune-suppressive tumor microenvironment. Loss of the Y chromosome (LOY) drives both phenotypes in bladder cancer (BC). We investigated the hypothesis that LOY leads to metabolic reprogramming using untargeted metabolomic profiling of human BC cells and analysis of pan-cancer transcriptomic datasets. This revealed that aerobic glycolysis is activated in LOY BC cells. Since prior work showed that expression of collagen receptor DDR2 drives BC progression and DDR2 is a regulator of tumor metabolism, we investigated if DDR2 is implicated in metabolic reprogramming of LOY-tumors. Analysis of scRNAseq data from 251 patients with 12 tumor types found that LOY and DDR2 expression promote aerobic glycolysis, and this was confirmed by metabolomics. Deletion of DDR2 in LOY BC cells reduced glycolytic flux, inhibited cell proliferation, reduced EMT and stemness features, and promoted apoptosis. Our data provide a rationale for using LOY as a tumor selection biomarker for DDR2 targeted therapeutics. TeaserLoss of the Y chromosome augments glycolytic metabolism in bladder cancer cells, and this is in part dependent on the collagen receptor DDR2.

cancer biology↗

bioRxiv2025

Structural insights and engineering of deep-sea halophilic PET hydrolytic enzymes

Pervasive use of polyethylene terephthalate (PET) poses tremendous challenges for global waste management and environmental sustainability, fueling growing interests in enzymatic degradation as an eco-friendly solution. While PET hydrolases hold significant promise, their industrial deployment is hindered by insufficient performance, particularly under high-salinity conditions raised from high substrate loads. Building on our previous discovery of three deep-sea PET hydrolases (dsPETase01, dsPETase05 and dsPETase06) with exceptional halophilicity and PET-degrading activity, we here present their three-dimensional structures and mechanistic characterization. Structural comparison, site-directed mutagenesis, and domain swapping reveal key structural features and the essential role of C-terminal acidic residues in salt tolerance. Integrating semi-rational protein design, Transformer-based modeling, and disulfide bond engineering, we synergistically enhance the thermostability and catalytic efficiency of dsPETase05. These findings elucidate the unique structural features and salt adaptation mechanisms of deep-sea halophilic PET hydrolases, and inform the future engineering of biocatalysts for application in harsh industrial environments.

molecular biology↗

bioRxiv2025

Large-Scale Neural Network Compensation Underlying Camouflaging in Trait Autism and Its Potential Mental Health Costs

Social camouflaging refers to strategies to hide or compensate for social difficulties, often at a significant mental health cost, and is particularly prevalent in autism. The large-scale neural network mechanisms underlying this adaptation remain poorly understood. This study aimed to identify these neural underpinnings and their link to other potential mental health issues. Using a dimensional approach, we recruited 110 healthy young adults who completed self-report questionnaires measuring autistic traits and camouflaging as well as depression and anxiety, and underwent resting-state fMRI scans. Using the 300-node Seitzman atlas encompassing 13 functional networks, we examined the interaction between camouflaging and autistic traits on brain network connectivity. Results showed that among individuals with higher autistic traits, greater camouflaging was associated with hyperconnectivities between the Default Mode (DMN) and Cingulo-Opercular Networks (CON), and within the CON. Crucially, DMN-CON hyperconnectivity mediated the relationship between camouflaging and potential mental health cost (i.e., depression and anxiety scores) but only in individuals with higher autistic traits. These findings reveal a specific neuro-compensatory mechanism underlying autistic camouflaging involving self-referential and executive control systems and provide a neurobiological explanation for its potential mental health burden, highlighting the need for societal changes that reduce the pressure for such adaptations. Lay AbstractSocial camouflaging refers to strategies autistic people often use to hide their social differences to better adapt to everyday social contexts. While it may help in the short term, this constant effort can be mentally exhausting and is often linked to severe anxiety and depression. However, little is known about how different brain networks work together to enable social camouflaging and might contribute to a greater risk of anxiety and depression. In this study, autistic traits were measured in 110 young healthy adults in addition to questionnaire-based measures of social camouflaging, anxiety, and depression. Additionally, brain activity was recorded using magnetic resonance imaging while they were resting and not doing any task. We found that, in people with higher autistic traits, social camouflaging was linked to stronger connections between the brain network involved in thinking about oneself (self-reflection; Default Mode Network) and the one in charge of maintaining goal-directed behavior (action control; Cingulo-Opercular Network), as well as stronger connections within the latter brain network. These stronger connections between the self-reflection network and action control network partly explained why camouflaging may be associated with higher levels of anxiety and depression. In short, autistic camouflaging seems to rely on a cognitively demanding neural compensatory process, which can take a toll on mental health. Understanding this underscores the importance of creating a more accepting society to support the well-being of autistic individuals.

neuroscience↗

bioRxiv2025

First Whole-Genome Chikungunya Virus Sequence Detected in Mosquitoes during the 2025 Foshan Outbreak: Evidence of Field Vector Infection and Transmission Potential in China

BackgroundSince July 2025, an outbreak of mosquito-borne chikungunya fever occurred in Foshan City, Guangdong Province, China. This was the second outbreak in China following the one that occurred in Dongguan City, Guangdong Province, in 2010. Moreover, the intensity of this outbreak was significantly greater than that of the previous one. Updates to 23 August, more than 10,000 human cases had been reported. Here, we present the first full genome sequence of the chikungunya virus (CHIKV) derived from field-trapped mosquitoes during the outbreak. MethodsAdult Aedes albopictus were BG-trap captured from residences and parklands in three hotspot towns with high density of confirmed human cases. Mosquitoes were morphologically identified and pooled by species, sex and environment types. RNA was extracted, screened by CHIKV RT-qPCR, then positive pools underwent sanger and whole-genome sequencing for complete sequences. Lineage and mutational profiles were inferred by maximum likelihood phylogenetic and comparison against human and mosquito genomes. The distribution of amino acid site mutations in different protein coding regions was also analyzed. ResultThrough 11 days of collection using 10 BG-traps, 2,803 mosquitoes were captured. 1569 (55.97%) female Ae. albopictus were divided into 77 pools and 9.09% (7/77) of the pools tested positive for CHIKV. The local Ae. albopictus minimum infection rate (MIR, per 1000 females) was 4.46, while the MIR for residences in Lecong Town was the highest at 9.17. The MIR for parklands was slight higher than for residences (4.60 vs. 4.30). All the 5 Ae. albopictus-derived complete CHIKV genome clustered within ECSA-Indian Ocean lineage genotype, closely related to human-derived genomes on 2025 Reunion Island. Amino-acid mutations E1-A226V/E2-L210Q were detected in the strains, which enhanced adaptability to Ae. albopictus and increased the transmission capacity. Novel mutation observed on E1 and E2 were totally consist to the patient-derived CHIKV in 2025 Reunion Island. ConclusionsIt was the first mosquito-derived CHIKV whole-genome during the 2025 Foshan outbreak, filling a critical gap between human case and entomological surveillance. Ae. albopictus was confirmed as the primary vector during the outbreak. The current outbreak CHIKV strain with particular amino-acid mutations had adapted to Ae. albopictus transmission. Compared to previous Chikungunya outbreaks over the past decade, the Foshan outbreak occurred earlier (early July), in a larger urban area (with a population of over 9.5 million), and with abundant breeding sites for the vector mosquito Ae. albopictus. However, the outbreak was quickly brought under control, with daily case numbers consistently decreasing, which is closely linked to the strong vector control measures implemented by the Chinese government in the early stages of the outbreak. Moreover, this event once again underscores the necessity of early monitoring of vector mosquitoes and the importance of implementing highly effective vector intervention measures as soon as possible after an outbreak occurs.

microbiology↗

bioRxiv2025

The Pulmonary Microbial Signatures of Early Stages of Severe Infection in Children

The respiratory tract related diseases are the main causes of death in children. Child pulmonary severe infection is the most important inducement for Respiratory tract related diseases. Therefore, it is necessary to understand the composition of the microbial community and the species correlation in children with severe pulmonary infection. In this study, the bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF) samples of 782 children with severe infection in the early stage were systematically analyzed by amplicon-sequencing technology to reveal the distribution of microbial community and its clinical correlation. Results reveal significantly higher bacterial abundance in BALF than in blood/cerebrospinal fluid, with community structures shaped by tissue microenvironments, geographical disparities, age, and clinical symptoms. Neonatal BALF harbors simplified microbiota dominated by probiotics, while diversity increases with age, showing marked differences between 1-3 and 6-12-year-olds. Sepsis samples exhibit reduced microbial diversity, with Staphylococcus and Moraxella enrichments in the CST-4 cluster. Respiratory symptom progression correlates with microbiota succession from oral colonizers to respiratory pathogens. Third-generation sequencing-derived co-occurrence networks illustrate synergistic interactions among opportunistic pathogens, providing a basis for ecological targeted therapy. This study provides a key basis for breaking through the limitations of traditional diagnosis, establishing a precise diagnosis and treatment system based on third-generation sequencing, and developing ecological targeted treatment strategies.

pathology↗

bioRxiv2025

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing data, we developed Seq2Karyotype (S2K), a tool that fits karyotype models with clonality estimation based on read-depth and allelic imbalance in a bulk sample and supports visualization-guided refinement. Analysis on 19 adult and pediatric cancer cell lines revealed unexpected intratumoral heterogeneity involving multiple copy number variation (CNV) states including whole-genome duplication, which were validated by imaging and single-cell omics profiling. Analyses on patient samples showed high concordance with clinical cytogenetic reports for acute myeloid leukemia, and revealed evolutionary trajectories from multi-region metastatic neuroblastomas implicating reversion. These findings highlight extensive and dynamic intratumoral heterogeneity contributed by CNV in both cell line models and patient samples, which may inform future research on tumor evolution under selective pressure such as drug exposure.

bioinformatics↗

bioRxiv2025

Tunable nucleofugality in carbamoyl-bearing covalent cholinesterase inhibitors

A handful of carbamate warheads is utilised in chemical biology to target serine hydrolases. The following case study on cholinesterases is the first comprehensive structure-reactivity exploration of the carbamoyl warhead, rather than one-target-oriented structure-activity study, with in-depth profiling of diverse halogen, chalcogen, and nitrogen-based leaving groups (nucleofuges) that can tune warhead reactivity. With computational tools we correlated the experimentally observed reactivities with steric and electronic factors of the investigated warheads. QM/MM simulations considering the enzymatic environment explained how substitution of carbon for nitrogen in the leaving groups of compounds 26 and 28 through resonance stabilisation, inductive bond polarization, and acidity amplification lowered the reaction barrier and increased the reaction rate >360 million times, making compound 28 a covalent inhibitor. Our findings underline the complexity of covalent inhibition and demonstrate that multiple complementary methods are required to interpret and predict covalent behaviour. Additionally, even though carbamates typically act as slow substrates, we were able to slow down decarbamoylation to a point where inhibition became de facto irreversible. The most interesting O-isoxazol-3-yl carbamate warhead was further profiled against the wider human proteome and showed low off-target reactivity, making it useful in further drug discovery. By establishing structure-reactivity principles for carbamoyl warhead, this study provides a generalisable framework for the development of selective covalent inhibitors and activity-based probes across diverse targets.

pharmacology and toxicology↗